The covalently bound diazo group as an infrared probe for hydrogen bonding environments.

Covalently bound diazo groups are frequently found in biomolecular substrates. The C[double bond, length as m-dash]N[double bond, length as m-dash]N asymmetric stretching vibration (νas) of the diazo group has a large extinction coefficient and appears in an uncongested spectral region. To evaluate the solvatochromism of the C[double bond, length as m-dash]N[double bond, length as m-dash]N νas band for studying biomolecules, we recorded the infrared (IR) spectra of a diazo model compound, 2-diazo-3-oxo-butyric acid ethyl ester, in different solvents. The width of the C[double bond, length as m-dash]N[double bond, length as m-dash]N νas band was linearly dependent on the Kamlet-Taft solvent parameter, which reflects the polarizability and hydrogen bond accepting ability of the solvent. Therefore, the width of the C[double bond, length as m-dash]N[double bond, length as m-dash]N νas band could be used to probe these properties for a solvent. We found that the position of the C[double bond, length as m-dash]N[double bond, length as m-dash]N νas band was linearly correlated with the density of hydrogen bond donor groups in the solvent. We studied the relaxation dynamics and spectral diffusion of the C[double bond, length as m-dash]N[double bond, length as m-dash]N νas band of a natural amino acid, 6-diazo-5-oxo-l-norleucine, in water using nonlinear IR spectroscopy. The relaxation and spectral diffusion time constants of the C[double bond, length as m-dash]N[double bond, length as m-dash]N νas band were similar to those of the N[double bond, length as m-dash]N[double bond, length as m-dash]N νas band. We concluded that the position and width of the C[double bond, length as m-dash]N[double bond, length as m-dash]N νas band of the diazo group could be used to probe the hydrogen bond donating and accepting ability of a solvent, respectively. These results suggest that the diazo group could be used as a site-specific IR probe for the local hydration environments.

[1]  H. W. Dion,et al.  6-Diazo-5-oxo-L-norleucine, A New Tumor-inhibitory Substance. II.1 Isolation and Characterization2 , 1956 .

[2]  J. Fugger,et al.  Aliphatic Diazo Compounds. III. Infrared Spectra1,2 , 1957 .

[3]  C. Pecile,et al.  Infra-red intensity measurements on diazocompounds , 1960 .

[4]  A. Meister,et al.  Affinity labeling of gamma-glutamyl transpeptidase and location of the gamma-glutamyl binding site on the light subunit. , 1977, Proceedings of the National Academy of Sciences of the United States of America.

[5]  R. Taft,et al.  Linear solvation energy relationships Solvent effects on some fluorescence probes , 1981 .

[6]  Michael H. Abraham,et al.  Linear solvation energy relationships. 23. A comprehensive collection of the solvatochromic parameters, .pi.*, .alpha., and .beta., and some methods for simplifying the generalized solvatochromic equation , 1983 .

[7]  P. Champion,et al.  Resonance Raman studies of isotopically labeled chloroperoxidase. , 1986, Biochemistry.

[8]  J Higinbotham,et al.  An analytical derivation of a popular approximation of the Voigt function for quantification of NMR spectra. , 2000, Journal of magnetic resonance.

[9]  J. Torres,et al.  Site‐specific examination of secondary structure and orientation determination in membrane proteins: The peptidic 13C18O group as a novel infrared probe , 2001, Biopolymers.

[10]  W. DeGrado,et al.  Time-resolved infrared study of the helix-coil transition using (13)C-labeled helical peptides. , 2001, Journal of the American Chemical Society.

[11]  W. DeGrado,et al.  Using nitrile-derivatized amino acids as infrared probes of local environment. , 2003, Journal of the American Chemical Society.

[12]  Jianping Wang,et al.  Two-dimensional infrared spectroscopy of the alanine dipeptide in aqueous solution. , 2005, The journal of physical chemistry. B.

[13]  S. Decatur.  Elucidation of residue-level structure and dynamics of polypeptides via isotope-edited infrared spectroscopy. , 2006, Accounts of chemical research.

[14]  I. Arkin.  Isotope-edited IR spectroscopy for the study of membrane proteins , 2006, Current Opinion in Chemical Biology.

[15]  D. Raleigh,et al.  Residue specific resolution of protein folding dynamics using isotope-edited infrared temperature jump spectroscopy. , 2007, Biochemistry.

[16]  A. Barth.  Infrared spectroscopy of proteins. , 2007, Biochimica et biophysica acta.

[17]  Ilya J. Finkelstein,et al.  Frequency-frequency correlation functions and apodization in two-dimensional infrared vibrational echo spectroscopy: a new approach. , 2007, The Journal of chemical physics.

[18]  A. Tokmakoff,et al.  Amide I two-dimensional infrared spectroscopy of proteins. , 2008, Accounts of chemical research.

[19]  Carlos R. Baiz,et al.  Two-dimensional infrared spectroscopy of metal carbonyls. , 2009, Accounts of chemical research.

[20]  R. Hochstrasser,et al.  2D-IR experiments and simulations of the coupling between amide-I and ionizable side chains in proteins: application to the Villin headpiece. , 2009, The journal of physical chemistry. B.

[21]  B. A. Lindquist,et al.  Nitrile groups as vibrational probes of biomolecular structure and dynamics: an overview. , 2009, Physical chemistry chemical physics : PCCP.

[22]  T. Sakmar,et al.  Tracking G-protein-coupled receptor activation using genetically encoded infrared probes , 2010, Nature.

[23]  J. Choi,et al.  Real-time probing of ion pairing dynamics with 2DIR spectroscopy. , 2010, Chemphyschem : a European journal of chemical physics and physical chemistry.

[24]  F. Allain,et al.  Recent advances in segmental isotope labeling of proteins: NMR applications to large proteins and glycoproteins , 2010, Journal of biomolecular NMR.

[25]  D. Raleigh,et al.  Azidohomoalanine: a conformationally sensitive IR probe of protein folding, protein structure, and electrostatics. , 2010, Angewandte Chemie.

[26]  M. Zanni,et al.  Residue-specific structural kinetics of proteins through the union of isotope labeling, mid-IR pulse shaping, and coherent 2D IR spectroscopy. , 2010, Methods.

[27]  Gonçalo J. L. Bernardes,et al.  CORM-3 reactivity toward proteins: the crystal structure of a Ru(II) dicarbonyl-lysozyme complex. , 2011, Journal of the American Chemical Society.

[28]  Christopher C. Nawrat,et al.  Natural products containing a diazo group. , 2011, Natural product reports.

[29]  M. Thielges,et al.  Dynamics of the folded and unfolded villin headpiece (HP35) measured with ultrafast 2D IR vibrational echo spectroscopy , 2011, Proceedings of the National Academy of Sciences.

[30]  R. Hochstrasser,et al.  Residue-Specific Vibrational Echoes Yield 3D Structures of a Transmembrane Helix Dimer , 2011, Science.

[31]  Martin T. Zanni,et al.  Concepts and Methods of 2D Infrared Spectroscopy , 2011 .

[32]  M. J. Tucker,et al.  2D IR photon echo of azido-probes for biomolecular dynamics. , 2011, Physical chemistry chemical physics : PCCP.

[33]  Jacob S. Lipkin,et al.  Modulating Accidental Fermi Resonance: What a Difference a Neutron Makes. , 2011, The journal of physical chemistry letters.

[34]  Feng Gai,et al.  Site-Specific Spectroscopic Reporters of the Local Electric Field, Hydration, Structure, and Dynamics of Biomolecules. , 2011, The journal of physical chemistry letters.

[35]  P. Schultz,et al.  Two-dimensional IR spectroscopy of protein dynamics using two vibrational labels: a site-specific genetically encoded unnatural amino acid and an active site ligand. , 2011, The journal of physical chemistry. B.

[36]  P. Dawson,et al.  Carbon−Deuterium Bonds as Site-Specific and Nonperturbative Probes for Time-Resolved Studies of Protein Dynamics and Folding , 2011 .

[37]  C. Londergan,et al.  Covalently bound azido groups are very specific water sensors, even in hydrogen-bonding environments. , 2012, The journal of physical chemistry. B.

[38]  Hiroaki Maekawa,et al.  Vibrational correlation between conjugated carbonyl and diazo modes studied by single- and dual-frequency two-dimensional infrared spectroscopy , 2013 .

[39]  M. Zanni,et al.  A strongly absorbing class of non-natural labels for probing protein electrostatics and solvation with FTIR and 2D IR spectroscopies. , 2013, The journal of physical chemistry. B.

[40]  S. Boxer,et al.  Measuring electrostatic fields in both hydrogen-bonding and non-hydrogen-bonding environments using carbonyl vibrational probes. , 2013, Journal of the American Chemical Society.

[41]  M. Cho,et al.  Infrared probes for studying the structure and dynamics of biomolecules. , 2013, Chemical reviews.

[42]  K. Brindle,et al.  Diazo group as a new chemical reporter for bioorthogonal labelling of biomolecules , 2014 .

[43]  S. Boxer,et al.  Measuring electric fields and noncovalent interactions using the vibrational stark effect. , 2015, Accounts of chemical research.

[44]  F. Gai,et al.  Site-specific infrared probes of proteins. , 2015, Annual review of physical chemistry.

[45]  P. Hamm,et al.  Fast infrared spectroscopy of protein dynamics: advancing sensitivity and selectivity. , 2015, Current opinion in structural biology.

[46]  R. Raines,et al.  Diazo Compounds: Versatile Tools for Chemical Biology. , 2016, ACS chemical biology.

[47]  Feng Gai,et al.  C≡N stretching vibration of 5-cyanotryptophan as an infrared probe of protein local environment: what determines its frequency? , 2016, Physical chemistry chemical physics : PCCP.

[48]  F. Gai,et al.  Kinetic Isotope Effect Provides Insight into the Vibrational Relaxation Mechanism of Aromatic Molecules: Application to Cyano-phenylalanine. , 2016, The journal of physical chemistry letters.